rs121918527
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP2PP3_ModeratePP5
The NM_031407.7(HUWE1):c.12559C>T(p.Arg4187Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000018 in 111,071 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R4187H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_031407.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HUWE1 | NM_031407.7 | c.12559C>T | p.Arg4187Cys | missense_variant | 81/84 | ENST00000262854.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HUWE1 | ENST00000262854.11 | c.12559C>T | p.Arg4187Cys | missense_variant | 81/84 | 1 | NM_031407.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000180 AC: 2AN: 111071Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33303
GnomAD4 exome Cov.: 28
GnomAD4 genome ? AF: 0.0000180 AC: 2AN: 111071Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33303
ClinVar
Submissions by phenotype
Intellectual disability, X-linked syndromic, Turner type Pathogenic:3
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2008 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Dec 14, 2023 | Criteria applied: PS4_MOD,PM5,PS3_SUP,PM2_SUP,PP1,PP2 - |
Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics Lab, CHRU Brest | - | - - |
not provided Pathogenic:2Uncertain:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2023 | Identified in multiple male family members with intellectual disability in published literature (Froyen et al., 2008); Published functional studies demonstrate a damaging effect on protein function (Opperman et al., 2017: Hunkeler et al., 2021); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19377476, 23871722, 29180823, 29307790, 27130160, 29118367, 18252223, 33948573, 32336296, 34314700, 28445732, 36111624, 37167062) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 15, 2021 | This variant is not present in population databases (ExAC no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies have shown that this variant affects HUWE1 protein function (PMID: 29118367). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt HUWE1 protein function. ClinVar contains an entry for this variant (Variation ID: 10678). This variant is also known as c.12229C>T (p.R4077C). This variant has been observed in individual(s) with intellectual disability (PMID: 18252223, 19377476). This sequence change replaces arginine with cysteine at codon 4187 of the HUWE1 protein (p.Arg4187Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. - |
Non-syndromic X-linked intellectual disability Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | May 25, 2020 | A hemizygous missense variant was identified, NM_031407.6(HUWE1):c.12559C>T in exon 81 of 84 of the HUWE1 gene. This substitution is predicted to create a major amino acid change from an arginine to a cysteine at position 4187 of the protein, NP_113584.3(HUWE1):p.(Arg4187Cys). The arginine at this position has very high conservation (100 vertebrates, UCSC), and is located within the HECT domain. In silico software predicts this variant to be damaging (Polyphen, SIFT, CADD, Mutation Taster) and the variant is not present in the gnomAD population database. It has been previously reported in patients with X-linked intellectual disability (ClinVar; Hu, H. et al. (2016)). It has also been shown to segregate with disease in one family (Froyen, G. et al. (2008)). In addition, functional studies showed decreased DNA repair capacity and hypersensitivity to oxidative stress in patient lymphoblastoid cells (Bosshard, M. et al. (2017)). A different variant in the same codon resulting in a change to a histidine has been reported as likely pathogenic (ClinVar; Niranjan, T. et al . (2015)). Based on information available at the time of curation, this variant has been classified as PATHOGENIC. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at